Table 1. The five different types of NN used in the paper.

No.	Model	Layer1#node	Layer2#node	#Parameters (million)
1	Dense	796	X	7.52 M
2	Dense	100	X	0.95 M
3	Dense	796	100	7.59 M
4	PPI/TF+dense	696 + 100 dense	X	1.01 M
5	PPI/TF+dense	696 + 100 dense	100	1.08 M

Note that No.1 and No.2 represent the same architecture (Figure 1A) using different number of hidden layer nodes. The 696 in the PPI/TF models is from 348 TFs + 348 PPI groups. The number of nodes in the Dense models corresponds to the number of nodes in PPI/TF models for comparison. The additional 100 dense in each model are manually selected.